chr2-70900649-C-A
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2BP7
The NM_012476.3(VAX2):c.28C>A(p.Arg10Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000888 in 1,125,960 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 8.9e-7 ( 0 hom. )
Consequence
VAX2
NM_012476.3 synonymous
NM_012476.3 synonymous
Scores
1
1
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.876
Publications
0 publications found
Genes affected
VAX2 (HGNC:12661): (ventral anterior homeobox 2) This gene encodes a homeobox protein and is almost exclusively expressed in the ventral portion of the retina during development. In mouse studies, this gene was found to be required for the correct formation of the optic fissure and other aspects of retinal development. [provided by RefSeq, Sep 2008]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP7
Synonymous conserved (PhyloP=0.876 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| VAX2 | NM_012476.3 | c.28C>A | p.Arg10Arg | synonymous_variant | Exon 1 of 3 | ENST00000234392.3 | NP_036608.1 | |
| VAX2 | XM_011532750.4 | c.28C>A | p.Arg10Arg | synonymous_variant | Exon 1 of 4 | XP_011531052.1 | ||
| VAX2 | XM_011532751.4 | c.28C>A | p.Arg10Arg | synonymous_variant | Exon 1 of 4 | XP_011531053.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| VAX2 | ENST00000234392.3 | c.28C>A | p.Arg10Arg | synonymous_variant | Exon 1 of 3 | 1 | NM_012476.3 | ENSP00000234392.2 | ||
| VAX2 | ENST00000432367.6 | n.-150C>A | upstream_gene_variant | 5 | ENSP00000405114.2 | |||||
| ENSG00000296671 | ENST00000741093.1 | n.-244G>T | upstream_gene_variant | |||||||
| ENSG00000296671 | ENST00000741094.1 | n.-180G>T | upstream_gene_variant |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 8.88e-7 AC: 1AN: 1125960Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 538128 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1125960
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
538128
show subpopulations
African (AFR)
AF:
AC:
0
AN:
23112
American (AMR)
AF:
AC:
0
AN:
8528
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
15174
East Asian (EAS)
AF:
AC:
0
AN:
26702
South Asian (SAS)
AF:
AC:
0
AN:
33962
European-Finnish (FIN)
AF:
AC:
0
AN:
25466
Middle Eastern (MID)
AF:
AC:
0
AN:
3044
European-Non Finnish (NFE)
AF:
AC:
1
AN:
944376
Other (OTH)
AF:
AC:
0
AN:
45596
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Uncertain
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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